diff --git a/.gitignore b/.gitignore
index 92c1e95c8..d47b1e991 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ jupyterhub_cookie_secret
 *.crt
 *.key
 doc/build
+doc/source/api
+doc/source/remoteappmanager_help.txt
\ No newline at end of file
diff --git a/COPYING.rst b/LICENSE.rst
similarity index 100%
rename from COPYING.rst
rename to LICENSE.rst
diff --git a/README.rst b/README.rst
index 7dad75b59..f160fbb8e 100644
--- a/README.rst
+++ b/README.rst
@@ -1,21 +1,24 @@
-Remote Application Manager
---------------------------
+Simphony-remote
+===============
 
 .. image:: https://readthedocs.org/projects/simphony-remote/badge/?version=latest
    :target: http://simphony-remote.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
-This software is developed under the SimPhoNy project, an EU-project funded by
-the 7th Framework Programme (Project number 604005) under the call
-NMP.2013.1.4-1: "Development of an integrated multi-scale modelling environment
-for nanomaterials and systems by design".
+The Simphony-remote is web service that allows users to start and work with simphony enabled environments remotely.
 
-The package provides an executable replacement of jupyterhub-singleuser, and
-provides management capabilities for docker images and containers. It is spawn
-by the jupyterhub server in response to a login.
+Key provided features:
 
-License 
--------
+   - Isolated working environments using docker containers.
+   - No install remote access through a web browser.
+   - Sharing of working sessions.
+   - Based on community supported open source initiatives (JupyterHub)
 
-This software is released under the terms of the BSD license. See the
-`COPYING.rst <COPYING.rst>`_ for license terms.
+
+Acknowledgments
+---------------
+
+This software is developed under the SimPhoNy project, an EU-project
+funded by the 7th Framework Programme (Project number 604005) under
+the call NMP.2013.1.4-1: "Development of an integrated multi-scale
+modelling environment for nanomaterials and systems by design".
diff --git a/doc/Makefile b/doc/Makefile
index 22a433c81..231fba10b 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -49,6 +49,7 @@ help:
 .PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf source/api
 
 .PHONY: html
 html:
diff --git a/doc/make.bat b/doc/make.bat
index 27b79f401..bb50358f6 100644
--- a/doc/make.bat
+++ b/doc/make.bat
@@ -48,6 +48,7 @@ if "%1" == "help" (
 if "%1" == "clean" (
 	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
 	del /q /s %BUILDDIR%\*
+	rmdir /q /s source\api
 	goto end
 )
 
diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
new file mode 100644
index 000000000..98cedd8dc
--- /dev/null
+++ b/doc/source/_extensions/__init__.py
@@ -0,0 +1,587 @@
+# -*- coding: utf-8 -*-
+"""
+    sphinx.ext.autosummary
+    ~~~~~~~~~~~~~~~~~~~~~~
+
+    Sphinx extension that adds an autosummary:: directive, which can be
+    used to generate function/method/attribute/etc. summary lists, similar
+    to those output eg. by Epydoc and other API doc generation tools.
+
+    An :autolink: role is also provided.
+
+    autosummary directive
+    ---------------------
+
+    The autosummary directive has the form::
+
+        .. autosummary::
+           :nosignatures:
+           :toctree: generated/
+
+           module.function_1
+           module.function_2
+           ...
+
+    and it generates an output table (containing signatures, optionally)
+
+        ========================  =============================================
+        module.function_1(args)   Summary line from the docstring of function_1
+        module.function_2(args)   Summary line from the docstring
+        ...
+        ========================  =============================================
+
+    If the :toctree: option is specified, files matching the function names
+    are inserted to the toctree with the given prefix:
+
+        generated/module.function_1
+        generated/module.function_2
+        ...
+
+    Note: The file names contain the module:: or currentmodule:: prefixes.
+
+    .. seealso:: autosummary_generate.py
+
+
+    autolink role
+    -------------
+
+    The autolink role functions as ``:obj:`` when the name referred can be
+    resolved to a Python object, and otherwise it becomes simple emphasis.
+    This can be used as the default role to make links 'smart'.
+
+    :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+"""
+
+import os
+import re
+import sys
+import inspect
+import posixpath
+from types import ModuleType
+
+from six import text_type
+from docutils.parsers.rst import directives
+from docutils.statemachine import ViewList
+from docutils import nodes
+
+import sphinx
+from sphinx import addnodes
+from sphinx.util.compat import Directive
+from sphinx.pycode import ModuleAnalyzer, PycodeError
+from sphinx.ext.autodoc import Options
+
+
+# -- autosummary_toc node ------------------------------------------------------
+
+class autosummary_toc(nodes.comment):
+    pass
+
+
+def process_autosummary_toc(app, doctree):
+    """Insert items described in autosummary:: to the TOC tree, but do
+    not generate the toctree:: list.
+    """
+    env = app.builder.env
+    crawled = {}
+
+    def crawl_toc(node, depth=1):
+        crawled[node] = True
+        for j, subnode in enumerate(node):
+            try:
+                if (isinstance(subnode, autosummary_toc) and
+                        isinstance(subnode[0], addnodes.toctree)):
+                    env.note_toctree(env.docname, subnode[0])
+                    continue
+            except IndexError:
+                continue
+            if not isinstance(subnode, nodes.section):
+                continue
+            if subnode not in crawled:
+                crawl_toc(subnode, depth+1)
+    crawl_toc(doctree)
+
+
+def autosummary_toc_visit_html(self, node):
+    """Hide autosummary toctree list in HTML output."""
+    raise nodes.SkipNode
+
+
+def autosummary_noop(self, node):
+    pass
+
+
+# -- autosummary_table node ----------------------------------------------------
+
+class autosummary_table(nodes.comment):
+    pass
+
+
+def autosummary_table_visit_html(self, node):
+    """Make the first column of the table non-breaking."""
+    try:
+        tbody = node[0][0][-1]
+        for row in tbody:
+            col1_entry = row[0]
+            par = col1_entry[0]
+            for j, subnode in enumerate(list(par)):
+                if isinstance(subnode, nodes.Text):
+                    new_text = text_type(subnode.astext())
+                    new_text = new_text.replace(u" ", u"\u00a0")
+                    par[j] = nodes.Text(new_text)
+    except IndexError:
+        pass
+
+
+# -- autodoc integration -------------------------------------------------------
+
+class FakeDirective:
+    env = {}
+    genopt = Options()
+
+
+def get_documenter(obj, parent):
+    """Get an autodoc.Documenter class suitable for documenting the given
+    object.
+
+    *obj* is the Python object to be documented, and *parent* is an
+    another Python object (e.g. a module or a class) to which *obj*
+    belongs to.
+    """
+    from sphinx.ext.autodoc import AutoDirective, DataDocumenter, \
+        ModuleDocumenter
+
+    if inspect.ismodule(obj):
+        # ModuleDocumenter.can_document_member always returns False
+        return ModuleDocumenter
+
+    # Construct a fake documenter for *parent*
+    if parent is not None:
+        parent_doc_cls = get_documenter(parent, None)
+    else:
+        parent_doc_cls = ModuleDocumenter
+
+    if hasattr(parent, '__name__'):
+        parent_doc = parent_doc_cls(FakeDirective(), parent.__name__)
+    else:
+        parent_doc = parent_doc_cls(FakeDirective(), "")
+
+    # Get the corrent documenter class for *obj*
+    classes = [cls for cls in AutoDirective._registry.values()
+               if cls.can_document_member(obj, '', False, parent_doc)]
+    if classes:
+        classes.sort(key=lambda cls: cls.priority)
+        return classes[-1]
+    else:
+        return DataDocumenter
+
+
+# -- .. autosummary:: ----------------------------------------------------------
+
+class Autosummary(Directive):
+    """
+    Pretty table containing short signatures and summaries of functions etc.
+
+    autosummary can also optionally generate a hidden toctree:: node.
+    """
+
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+    has_content = True
+    option_spec = {
+        'toctree': directives.unchanged,
+        'nosignatures': directives.flag,
+        'template': directives.unchanged,
+    }
+
+    def warn(self, msg):
+        self.warnings.append(self.state.document.reporter.warning(
+            msg, line=self.lineno))
+
+    def run(self):
+        self.env = env = self.state.document.settings.env
+        self.genopt = Options()
+        self.warnings = []
+        self.result = ViewList()
+
+        names = [x.strip().split()[0] for x in self.content
+                 if x.strip() and re.search(r'^[~a-zA-Z_]', x.strip()[0])]
+        items = self.get_items(names)
+        nodes = self.get_table(items)
+
+        if 'toctree' in self.options:
+            dirname = posixpath.dirname(env.docname)
+
+            tree_prefix = self.options['toctree'].strip()
+            docnames = []
+            for name, sig, summary, real_name in items:
+                docname = posixpath.join(tree_prefix, real_name)
+                docname = posixpath.normpath(posixpath.join(dirname, docname))
+                if docname not in env.found_docs:
+                    self.warn('toctree references unknown document %r'
+                              % docname)
+                docnames.append(docname)
+
+            tocnode = addnodes.toctree()
+            tocnode['includefiles'] = docnames
+            tocnode['entries'] = [(None, docn) for docn in docnames]
+            tocnode['maxdepth'] = -1
+            tocnode['glob'] = None
+
+            tocnode = autosummary_toc('', '', tocnode)
+            nodes.append(tocnode)
+
+        return self.warnings + nodes
+
+    def get_items(self, names):
+        """Try to import the given names, and return a list of
+        ``[(name, signature, summary_string, real_name), ...]``.
+        """
+        env = self.state.document.settings.env
+
+        prefixes = get_import_prefixes_from_env(env)
+
+        items = []
+
+        max_item_chars = 50
+
+        for name in names:
+            display_name = name
+            if name.startswith('~'):
+                name = name[1:]
+                display_name = name.split('.')[-1]
+
+            try:
+                real_name, obj, parent, modname = import_by_name(name, prefixes=prefixes)
+            except ImportError:
+                self.warn('failed to import %s' % name)
+                items.append((name, '', '', name))
+                continue
+
+            self.result = ViewList()  # initialize for each documenter
+            full_name = real_name
+            if not isinstance(obj, ModuleType):
+                # give explicitly separated module name, so that members
+                # of inner classes can be documented
+                full_name = modname + '::' + full_name[len(modname)+1:]
+            # NB. using full_name here is important, since Documenters
+            #     handle module prefixes slightly differently
+            documenter = get_documenter(obj, parent)(self, full_name)
+            if not documenter.parse_name():
+                self.warn('failed to parse name %s' % real_name)
+                items.append((display_name, '', '', real_name))
+                continue
+            if not documenter.import_object():
+                self.warn('failed to import object %s' % real_name)
+                items.append((display_name, '', '', real_name))
+                continue
+            if documenter.options.members and not documenter.check_module():
+                continue
+
+            # try to also get a source code analyzer for attribute docs
+            try:
+                documenter.analyzer = ModuleAnalyzer.for_module(
+                    documenter.get_real_modname())
+                # parse right now, to get PycodeErrors on parsing (results will
+                # be cached anyway)
+                documenter.analyzer.find_attr_docs()
+            except PycodeError as err:
+                documenter.env.app.debug(
+                    '[autodoc] module analyzer failed: %s', err)
+                # no source file -- e.g. for builtin and C modules
+                documenter.analyzer = None
+
+            # -- Grab the signature
+
+            sig = documenter.format_signature()
+            if not sig:
+                sig = ''
+            else:
+                max_chars = max(10, max_item_chars - len(display_name))
+                sig = mangle_signature(sig, max_chars=max_chars)
+                sig = sig.replace('*', r'\*')
+
+            # -- Grab the summary
+
+            documenter.add_content(None)
+            doc = list(documenter.process_doc([self.result.data]))
+
+            while doc and not doc[0].strip():
+                doc.pop(0)
+
+            # If there's a blank line, then we can assume the first sentence /
+            # paragraph has ended, so anything after shouldn't be part of the
+            # summary
+            for i, piece in enumerate(doc):
+                if not piece.strip():
+                    doc = doc[:i]
+                    break
+
+            # Try to find the "first sentence", which may span multiple lines
+            m = re.search(r"^([A-Z].*?\.)(?:\s|$)", " ".join(doc).strip())
+            if m:
+                summary = m.group(1).strip()
+            elif doc:
+                summary = doc[0].strip()
+            else:
+                summary = ''
+
+            items.append((display_name, sig, summary, real_name))
+
+        return items
+
+    def get_table(self, items):
+        """Generate a proper list of table nodes for autosummary:: directive.
+
+        *items* is a list produced by :meth:`get_items`.
+        """
+        table_spec = addnodes.tabular_col_spec()
+        table_spec['spec'] = 'p{0.5\linewidth}p{0.5\linewidth}'
+
+        table = autosummary_table('')
+        real_table = nodes.table('', classes=['longtable'])
+        table.append(real_table)
+        group = nodes.tgroup('', cols=2)
+        real_table.append(group)
+        group.append(nodes.colspec('', colwidth=10))
+        group.append(nodes.colspec('', colwidth=90))
+        body = nodes.tbody('')
+        group.append(body)
+
+        def append_row(*column_texts):
+            row = nodes.row('')
+            for text in column_texts:
+                node = nodes.paragraph('')
+                vl = ViewList()
+                vl.append(text, '<autosummary>')
+                self.state.nested_parse(vl, 0, node)
+                try:
+                    if isinstance(node[0], nodes.paragraph):
+                        node = node[0]
+                except IndexError:
+                    pass
+                row.append(nodes.entry('', node))
+            body.append(row)
+
+        for name, sig, summary, real_name in items:
+            qualifier = 'obj'
+            if 'nosignatures' not in self.options:
+                col1 = ':%s:`%s <%s>`\ %s' % (qualifier, name, real_name, sig)
+            else:
+                col1 = ':%s:`%s <%s>`' % (qualifier, name, real_name)
+            col2 = summary
+            append_row(col1, col2)
+
+        return [table_spec, table]
+
+
+def mangle_signature(sig, max_chars=30):
+    """Reformat a function signature to a more compact form."""
+    s = re.sub(r"^\((.*)\)$", r"\1", sig).strip()
+
+    # Strip strings (which can contain things that confuse the code below)
+    s = re.sub(r"\\\\", "", s)
+    s = re.sub(r"\\'", "", s)
+    s = re.sub(r"'[^']*'", "", s)
+
+    # Parse the signature to arguments + options
+    args = []
+    opts = []
+
+    opt_re = re.compile(r"^(.*, |)([a-zA-Z0-9_*]+)=")
+    while s:
+        m = opt_re.search(s)
+        if not m:
+            # The rest are arguments
+            args = s.split(', ')
+            break
+
+        opts.insert(0, m.group(2))
+        s = m.group(1)[:-2]
+
+    # Produce a more compact signature
+    sig = limited_join(", ", args, max_chars=max_chars-2)
+    if opts:
+        if not sig:
+            sig = "[%s]" % limited_join(", ", opts, max_chars=max_chars-4)
+        elif len(sig) < max_chars - 4 - 2 - 3:
+            sig += "[, %s]" % limited_join(", ", opts,
+                                           max_chars=max_chars-len(sig)-4-2)
+
+    return u"(%s)" % sig
+
+
+def limited_join(sep, items, max_chars=30, overflow_marker="..."):
+    """Join a number of strings to one, limiting the length to *max_chars*.
+
+    If the string overflows this limit, replace the last fitting item by
+    *overflow_marker*.
+
+    Returns: joined_string
+    """
+    full_str = sep.join(items)
+    if len(full_str) < max_chars:
+        return full_str
+
+    n_chars = 0
+    n_items = 0
+    for j, item in enumerate(items):
+        n_chars += len(item) + len(sep)
+        if n_chars < max_chars - len(overflow_marker):
+            n_items += 1
+        else:
+            break
+
+    return sep.join(list(items[:n_items]) + [overflow_marker])
+
+
+# -- Importing items -----------------------------------------------------------
+
+def get_import_prefixes_from_env(env):
+    """
+    Obtain current Python import prefixes (for `import_by_name`)
+    from ``document.env``
+    """
+    prefixes = [None]
+
+    currmodule = env.ref_context.get('py:module')
+    if currmodule:
+        prefixes.insert(0, currmodule)
+
+    currclass = env.ref_context.get('py:class')
+    if currclass:
+        if currmodule:
+            prefixes.insert(0, currmodule + "." + currclass)
+        else:
+            prefixes.insert(0, currclass)
+
+    return prefixes
+
+
+def import_by_name(name, prefixes=[None]):
+    """Import a Python object that has the given *name*, under one of the
+    *prefixes*.  The first name that succeeds is used.
+    """
+    tried = []
+    for prefix in prefixes:
+        try:
+            if prefix:
+                prefixed_name = '.'.join([prefix, name])
+            else:
+                prefixed_name = name
+            obj, parent, modname = _import_by_name(prefixed_name)
+            return prefixed_name, obj, parent, modname
+        except ImportError:
+            tried.append(prefixed_name)
+    raise ImportError('no module named %s' % ' or '.join(tried))
+
+
+def _import_by_name(name):
+    """Import a Python object given its full name."""
+    try:
+        name_parts = name.split('.')
+
+        # try first interpret `name` as MODNAME.OBJ
+        modname = '.'.join(name_parts[:-1])
+        if modname:
+            try:
+                __import__(modname)
+                mod = sys.modules[modname]
+                return getattr(mod, name_parts[-1]), mod, modname
+            except (ImportError, IndexError, AttributeError):
+                pass
+
+        # ... then as MODNAME, MODNAME.OBJ1, MODNAME.OBJ1.OBJ2, ...
+        last_j = 0
+        modname = None
+        for j in reversed(range(1, len(name_parts)+1)):
+            last_j = j
+            modname = '.'.join(name_parts[:j])
+            try:
+                __import__(modname)
+            except ImportError:
+                continue
+            if modname in sys.modules:
+                break
+
+        if last_j < len(name_parts):
+            parent = None
+            obj = sys.modules[modname]
+            for obj_name in name_parts[last_j:]:
+                parent = obj
+                obj = getattr(obj, obj_name)
+            return obj, parent, modname
+        else:
+            return sys.modules[modname], None, modname
+    except (ValueError, ImportError, AttributeError, KeyError) as e:
+        raise ImportError(*e.args)
+
+
+# -- :autolink: (smart default role) -------------------------------------------
+
+def autolink_role(typ, rawtext, etext, lineno, inliner,
+                  options={}, content=[]):
+    """Smart linking role.
+
+    Expands to ':obj:`text`' if `text` is an object that can be imported;
+    otherwise expands to '*text*'.
+    """
+    env = inliner.document.settings.env
+    r = env.get_domain('py').role('obj')(
+        'obj', rawtext, etext, lineno, inliner, options, content)
+    pnode = r[0][0]
+
+    prefixes = get_import_prefixes_from_env(env)
+    try:
+        name, obj, parent, modname = import_by_name(pnode['reftarget'], prefixes)
+    except ImportError:
+        content = pnode[0]
+        r[0][0] = nodes.emphasis(rawtext, content[0].astext(),
+                                 classes=content['classes'])
+    return r
+
+
+def process_generate_options(app):
+    genfiles = app.config.autosummary_generate
+
+    if genfiles and not hasattr(genfiles, '__len__'):
+        env = app.builder.env
+        genfiles = [env.doc2path(x, base=None) for x in env.found_docs
+                    if os.path.isfile(env.doc2path(x))]
+
+    if not genfiles:
+        return
+
+    from .generate import generate_autosummary_docs
+
+    ext = app.config.source_suffix[0]
+    genfiles = [genfile + (not genfile.endswith(ext) and ext or '')
+                for genfile in genfiles]
+
+    generate_autosummary_docs(genfiles, builder=app.builder,
+                              warn=app.warn, info=app.info, suffix=ext,
+                              base_path=app.srcdir)
+
+
+def setup(app):
+    # I need autodoc
+    app.setup_extension('sphinx.ext.autodoc')
+    app.add_node(autosummary_toc,
+                 html=(autosummary_toc_visit_html, autosummary_noop),
+                 latex=(autosummary_noop, autosummary_noop),
+                 text=(autosummary_noop, autosummary_noop),
+                 man=(autosummary_noop, autosummary_noop),
+                 texinfo=(autosummary_noop, autosummary_noop))
+    app.add_node(autosummary_table,
+                 html=(autosummary_table_visit_html, autosummary_noop),
+                 latex=(autosummary_noop, autosummary_noop),
+                 text=(autosummary_noop, autosummary_noop),
+                 man=(autosummary_noop, autosummary_noop),
+                 texinfo=(autosummary_noop, autosummary_noop))
+    app.add_directive('autosummary', Autosummary)
+    app.add_role('autolink', autolink_role)
+    app.connect('doctree-read', process_autosummary_toc)
+    app.connect('builder-inited', process_generate_options)
+    app.add_config_value('autosummary_generate', [], True, [bool])
+    return {'version': sphinx.__display_version__, 'parallel_read_safe': True}
diff --git a/doc/source/_extensions/generate.py b/doc/source/_extensions/generate.py
new file mode 100644
index 000000000..ba511f0ab
--- /dev/null
+++ b/doc/source/_extensions/generate.py
@@ -0,0 +1,348 @@
+# -*- coding: utf-8 -*-
+"""
+    sphinx.ext.autosummary.generate
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    Usable as a library or script to generate automatic RST source files for
+    items referred to in autosummary:: directives.
+
+    Each generated RST file contains a single auto*:: directive which
+    extracts the docstring of the referred item.
+
+    Example Makefile rule::
+
+       generate:
+               sphinx-autogen -o source/generated source/*.rst
+
+    :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+"""
+from __future__ import print_function
+
+import os
+import re
+import sys
+import pydoc
+import optparse
+import codecs
+
+from jinja2 import FileSystemLoader, TemplateNotFound
+from jinja2.sandbox import SandboxedEnvironment
+
+from sphinx import package_dir
+from . import import_by_name, get_documenter
+from sphinx.jinja2glue import BuiltinTemplateLoader
+from sphinx.util.osutil import ensuredir
+from sphinx.util.inspect import safe_getattr
+
+# Add documenters to AutoDirective registry
+from sphinx.ext.autodoc import add_documenter, \
+    ModuleDocumenter, ClassDocumenter, ExceptionDocumenter, DataDocumenter, \
+    FunctionDocumenter, MethodDocumenter, AttributeDocumenter, \
+    InstanceAttributeDocumenter
+add_documenter(ModuleDocumenter)
+add_documenter(ClassDocumenter)
+add_documenter(ExceptionDocumenter)
+add_documenter(DataDocumenter)
+add_documenter(FunctionDocumenter)
+add_documenter(MethodDocumenter)
+add_documenter(AttributeDocumenter)
+add_documenter(InstanceAttributeDocumenter)
+
+
+def main(argv=sys.argv):
+    usage = """%prog [OPTIONS] SOURCEFILE ..."""
+    p = optparse.OptionParser(usage.strip())
+    p.add_option("-o", "--output-dir", action="store", type="string",
+                 dest="output_dir", default=None,
+                 help="Directory to place all output in")
+    p.add_option("-s", "--suffix", action="store", type="string",
+                 dest="suffix", default="rst",
+                 help="Default suffix for files (default: %default)")
+    p.add_option("-t", "--templates", action="store", type="string",
+                 dest="templates", default=None,
+                 help="Custom template directory (default: %default)")
+    options, args = p.parse_args(argv[1:])
+
+    if len(args) < 1:
+        p.error('no input files given')
+
+    generate_autosummary_docs(args, options.output_dir,
+                              "." + options.suffix,
+                              template_dir=options.templates)
+
+
+def _simple_info(msg):
+    print(msg)
+
+
+def _simple_warn(msg):
+    print('WARNING: ' + msg, file=sys.stderr)
+
+
+# -- Generating output ---------------------------------------------------------
+
+def generate_autosummary_docs(sources, output_dir=None, suffix='.rst',
+                              warn=_simple_warn, info=_simple_info,
+                              base_path=None, builder=None, template_dir=None):
+
+    showed_sources = list(sorted(sources))
+    if len(showed_sources) > 20:
+        showed_sources = showed_sources[:10] + ['...'] + showed_sources[-10:]
+    info('[autosummary] generating autosummary for: %s' %
+         ', '.join(showed_sources))
+
+    if output_dir:
+        info('[autosummary] writing to %s' % output_dir)
+
+    if base_path is not None:
+        sources = [os.path.join(base_path, filename) for filename in sources]
+
+    # create our own templating environment
+    template_dirs = [os.path.join(package_dir, 'ext',
+                                  'autosummary', 'templates')]
+    if builder is not None:
+        # allow the user to override the templates
+        template_loader = BuiltinTemplateLoader()
+        template_loader.init(builder, dirs=template_dirs)
+    else:
+        if template_dir:
+            template_dirs.insert(0, template_dir)
+        template_loader = FileSystemLoader(template_dirs)
+    template_env = SandboxedEnvironment(loader=template_loader)
+
+    # read
+    items = find_autosummary_in_files(sources)
+
+    # keep track of new files
+    new_files = []
+
+    # write
+    for name, path, template_name in sorted(set(items), key=str):
+        if path is None:
+            # The corresponding autosummary:: directive did not have
+            # a :toctree: option
+            continue
+
+        path = output_dir or os.path.abspath(path)
+        ensuredir(path)
+
+        try:
+            name, obj, parent, mod_name = import_by_name(name)
+        except ImportError as e:
+            warn('[autosummary] failed to import %r: %s' % (name, e))
+            continue
+
+        fn = os.path.join(path, name + suffix)
+
+        # skip it if it exists
+        if os.path.isfile(fn):
+            continue
+
+        new_files.append(fn)
+
+        with open(fn, 'w') as f:
+            doc = get_documenter(obj, parent)
+
+            if template_name is not None:
+                template = template_env.get_template(template_name)
+            else:
+                try:
+                    template = template_env.get_template('autosummary/%s.rst'
+                                                         % doc.objtype)
+                except TemplateNotFound:
+                    template = template_env.get_template('autosummary/base.rst')
+
+            # Patched get_members according to
+            # http://stackoverflow.com/questions/25405110/sphinx-autosummary-with-toctree-also-lists-imported-members/25460763#25460763
+            def get_members(obj, typ, include_public=[], imported=False):
+                items = []
+                for name in dir(obj):
+                    try:
+                        obj_name = safe_getattr(obj, name)
+                        documenter = get_documenter(obj_name, obj)
+                    except AttributeError:
+                        continue
+                    if documenter.objtype == typ:
+                        try:
+                            cond = (
+                                imported or
+                                obj_name.__module__ == obj.__name__
+                                )
+                        except AttributeError:
+                            cond = True
+                        if cond:
+                            items.append(name)
+                public = [x for x in items
+                          if x in include_public or not x.startswith('_')]
+                return public, items
+
+            ns = {}
+
+            if doc.objtype == 'module':
+                ns['members'] = dir(obj)
+                ns['functions'], ns['all_functions'] = \
+                    get_members(obj, 'function')
+                ns['classes'], ns['all_classes'] = \
+                    get_members(obj, 'class')
+                ns['exceptions'], ns['all_exceptions'] = \
+                    get_members(obj, 'exception')
+            elif doc.objtype == 'class':
+                ns['members'] = dir(obj)
+                ns['methods'], ns['all_methods'] = \
+                    get_members(obj, 'method', ['__init__'])
+                ns['attributes'], ns['all_attributes'] = \
+                    get_members(obj, 'attribute')
+
+            parts = name.split('.')
+            if doc.objtype in ('method', 'attribute'):
+                mod_name = '.'.join(parts[:-2])
+                cls_name = parts[-2]
+                obj_name = '.'.join(parts[-2:])
+                ns['class'] = cls_name
+            else:
+                mod_name, obj_name = '.'.join(parts[:-1]), parts[-1]
+
+            ns['fullname'] = name
+            ns['module'] = mod_name
+            ns['objname'] = obj_name
+            ns['name'] = parts[-1]
+
+            ns['objtype'] = doc.objtype
+            ns['underline'] = len(name) * '='
+
+            rendered = template.render(**ns)
+            f.write(rendered)
+
+    # descend recursively to new files
+    if new_files:
+        generate_autosummary_docs(new_files, output_dir=output_dir,
+                                  suffix=suffix, warn=warn, info=info,
+                                  base_path=base_path, builder=builder,
+                                  template_dir=template_dir)
+
+
+# -- Finding documented entries in files ---------------------------------------
+
+def find_autosummary_in_files(filenames):
+    """Find out what items are documented in source/*.rst.
+
+    See `find_autosummary_in_lines`.
+    """
+    documented = []
+    for filename in filenames:
+        with codecs.open(filename, 'r', encoding='utf-8',
+                         errors='ignore') as f:
+            lines = f.read().splitlines()
+            documented.extend(find_autosummary_in_lines(lines,
+                                                        filename=filename))
+    return documented
+
+
+def find_autosummary_in_docstring(name, module=None, filename=None):
+    """Find out what items are documented in the given object's docstring.
+
+    See `find_autosummary_in_lines`.
+    """
+    try:
+        real_name, obj, parent, modname = import_by_name(name)
+        lines = pydoc.getdoc(obj).splitlines()
+        return find_autosummary_in_lines(lines, module=name, filename=filename)
+    except AttributeError:
+        pass
+    except ImportError as e:
+        print("Failed to import '%s': %s" % (name, e))
+    except SystemExit as e:
+        print("Failed to import '%s'; the module executes module level "
+              "statement and it might call sys.exit()." % name)
+    return []
+
+
+def find_autosummary_in_lines(lines, module=None, filename=None):
+    """Find out what items appear in autosummary:: directives in the
+    given lines.
+
+    Returns a list of (name, toctree, template) where *name* is a name
+    of an object and *toctree* the :toctree: path of the corresponding
+    autosummary directive (relative to the root of the file name), and
+    *template* the value of the :template: option. *toctree* and
+    *template* ``None`` if the directive does not have the
+    corresponding options set.
+    """
+    autosummary_re = re.compile(r'^(\s*)\.\.\s+autosummary::\s*')
+    automodule_re = re.compile(
+        r'^\s*\.\.\s+automodule::\s*([A-Za-z0-9_.]+)\s*$')
+    module_re = re.compile(
+        r'^\s*\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
+    autosummary_item_re = re.compile(r'^\s+(~?[_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')
+    toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
+    template_arg_re = re.compile(r'^\s+:template:\s*(.*?)\s*$')
+
+    documented = []
+
+    toctree = None
+    template = None
+    current_module = module
+    in_autosummary = False
+    base_indent = ""
+
+    for line in lines:
+        if in_autosummary:
+            m = toctree_arg_re.match(line)
+            if m:
+                toctree = m.group(1)
+                if filename:
+                    toctree = os.path.join(os.path.dirname(filename),
+                                           toctree)
+                continue
+
+            m = template_arg_re.match(line)
+            if m:
+                template = m.group(1).strip()
+                continue
+
+            if line.strip().startswith(':'):
+                continue  # skip options
+
+            m = autosummary_item_re.match(line)
+            if m:
+                name = m.group(1).strip()
+                if name.startswith('~'):
+                    name = name[1:]
+                if current_module and \
+                   not name.startswith(current_module + '.'):
+                    name = "%s.%s" % (current_module, name)
+                documented.append((name, toctree, template))
+                continue
+
+            if not line.strip() or line.startswith(base_indent + " "):
+                continue
+
+            in_autosummary = False
+
+        m = autosummary_re.match(line)
+        if m:
+            in_autosummary = True
+            base_indent = m.group(1)
+            toctree = None
+            template = None
+            continue
+
+        m = automodule_re.search(line)
+        if m:
+            current_module = m.group(1).strip()
+            # recurse into the automodule docstring
+            documented.extend(find_autosummary_in_docstring(
+                current_module, filename=filename))
+            continue
+
+        m = module_re.match(line)
+        if m:
+            current_module = m.group(2)
+            continue
+
+    return documented
+
+
+if __name__ == '__main__':
+    main()
diff --git a/doc/source/_templates/module_template.rst b/doc/source/_templates/module_template.rst
new file mode 100644
index 000000000..9f18aeeaf
--- /dev/null
+++ b/doc/source/_templates/module_template.rst
@@ -0,0 +1,61 @@
+{{ name }}
+{{ underline }}
+
+.. currentmodule:: {{ fullname }}
+.. module:: {{ fullname }}
+
+{% block functions %}
+{% if functions %}
+.. rubric:: Functions
+
+.. autosummary::
+{% for item in functions %}
+   {{ item }}
+{%- endfor %}
+
+|
+|
+
+{% for item in functions %}
+.. autofunction:: {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+{% block classes %}
+{% if classes %}
+.. rubric:: Classes
+
+.. autosummary::
+
+{% for item in classes %}
+   {{ item }}
+{%- endfor %}
+
+|
+|
+
+{% for item in classes %}
+.. autoclass:: {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
+
+{% block exceptions %}
+{% if exceptions %}
+.. rubric:: Exceptions
+
+.. autosummary::
+
+{% for item in exceptions %}
+   {{ item }}
+{%- endfor %}
+
+|
+|
+
+{% for item in exceptions %}
+.. autoclass:: {{ item }}
+
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/doc/source/api.rst b/doc/source/api.rst
deleted file mode 100644
index a26d1201e..000000000
--- a/doc/source/api.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-API 
-===
-
-.. toctree::
-   :maxdepth: 4
-
-   api/remoteappmanager
diff --git a/doc/source/api/remoteappmanager.cli.remoteappdb.rst b/doc/source/api/remoteappmanager.cli.remoteappdb.rst
deleted file mode 100644
index a73c511d1..000000000
--- a/doc/source/api/remoteappmanager.cli.remoteappdb.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-remoteappmanager.cli.remoteappdb package
-========================================
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.cli.remoteappdb
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.cli.remoteapprest.rst b/doc/source/api/remoteappmanager.cli.remoteapprest.rst
deleted file mode 100644
index 736b8c8d4..000000000
--- a/doc/source/api/remoteappmanager.cli.remoteapprest.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-remoteappmanager.cli.remoteapprest package
-==========================================
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.cli.remoteapprest
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.cli.rst b/doc/source/api/remoteappmanager.cli.rst
deleted file mode 100644
index 86d1cd916..000000000
--- a/doc/source/api/remoteappmanager.cli.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-remoteappmanager.cli package
-============================
-
-Subpackages
------------
-
-.. toctree::
-
-    remoteappmanager.cli.remoteappdb
-    remoteappmanager.cli.remoteapprest
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.cli
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.db.rst b/doc/source/api/remoteappmanager.db.rst
deleted file mode 100644
index e33719b6c..000000000
--- a/doc/source/api/remoteappmanager.db.rst
+++ /dev/null
@@ -1,42 +0,0 @@
-remoteappmanager.db package
-===========================
-
-Submodules
-----------
-
-remoteappmanager.db.csv_db module
----------------------------------
-
-.. automodule:: remoteappmanager.db.csv_db
-    :members:
-    :special-members: __init__
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.db.interfaces module
--------------------------------------
-
-.. automodule:: remoteappmanager.db.interfaces
-    :members:
-    :special-members: __init__
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.db.orm module
-------------------------------
-
-.. automodule:: remoteappmanager.db.orm
-    :members:
-    :special-members: __init__
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.db
-    :members:
-    :special-members: __init__
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.docker.rst b/doc/source/api/remoteappmanager.docker.rst
deleted file mode 100644
index 80644a4cb..000000000
--- a/doc/source/api/remoteappmanager.docker.rst
+++ /dev/null
@@ -1,54 +0,0 @@
-remoteappmanager.docker package
-===============================
-
-Submodules
-----------
-
-remoteappmanager.docker.async_docker_client module
---------------------------------------------------
-
-.. automodule:: remoteappmanager.docker.async_docker_client
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.docker.container module
-----------------------------------------
-
-.. automodule:: remoteappmanager.docker.container
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.docker.container_manager module
-------------------------------------------------
-
-.. automodule:: remoteappmanager.docker.container_manager
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.docker.docker_labels module
---------------------------------------------
-
-.. automodule:: remoteappmanager.docker.docker_labels
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.docker.image module
-------------------------------------
-
-.. automodule:: remoteappmanager.docker.image
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.docker
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.handlers.rst b/doc/source/api/remoteappmanager.handlers.rst
deleted file mode 100644
index c94faaf6a..000000000
--- a/doc/source/api/remoteappmanager.handlers.rst
+++ /dev/null
@@ -1,38 +0,0 @@
-remoteappmanager.handlers package
-=================================
-
-Submodules
-----------
-
-remoteappmanager.handlers.api module
-------------------------------------
-
-.. automodule:: remoteappmanager.handlers.api
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.handlers.base_handler module
----------------------------------------------
-
-.. automodule:: remoteappmanager.handlers.base_handler
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.handlers.home_handler module
----------------------------------------------
-
-.. automodule:: remoteappmanager.handlers.home_handler
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.handlers
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.logging.rst b/doc/source/api/remoteappmanager.logging.rst
deleted file mode 100644
index 2d362ce34..000000000
--- a/doc/source/api/remoteappmanager.logging.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-remoteappmanager.logging package
-================================
-
-Submodules
-----------
-
-remoteappmanager.logging.logging_mixin module
----------------------------------------------
-
-.. automodule:: remoteappmanager.logging.logging_mixin
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.logging
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.rest.http.rst b/doc/source/api/remoteappmanager.rest.http.rst
deleted file mode 100644
index d045864d9..000000000
--- a/doc/source/api/remoteappmanager.rest.http.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-remoteappmanager.rest.http package
-==================================
-
-Submodules
-----------
-
-remoteappmanager.rest.http.httpstatus module
---------------------------------------------
-
-.. automodule:: remoteappmanager.rest.http.httpstatus
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.rest.http.payloaded_http_error module
-------------------------------------------------------
-
-.. automodule:: remoteappmanager.rest.http.payloaded_http_error
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.rest.http
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.rest.rst b/doc/source/api/remoteappmanager.rest.rst
deleted file mode 100644
index 5615c69a1..000000000
--- a/doc/source/api/remoteappmanager.rest.rst
+++ /dev/null
@@ -1,53 +0,0 @@
-remoteappmanager.rest package
-=============================
-
-Subpackages
------------
-
-.. toctree::
-
-    remoteappmanager.rest.http
-
-Submodules
-----------
-
-remoteappmanager.rest.exceptions module
----------------------------------------
-
-.. automodule:: remoteappmanager.rest.exceptions
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.rest.registry module
--------------------------------------
-
-.. automodule:: remoteappmanager.rest.registry
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.rest.resource module
--------------------------------------
-
-.. automodule:: remoteappmanager.rest.resource
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.rest.rest_handler module
------------------------------------------
-
-.. automodule:: remoteappmanager.rest.rest_handler
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.rest
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.restresources.rst b/doc/source/api/remoteappmanager.restresources.rst
deleted file mode 100644
index ead031892..000000000
--- a/doc/source/api/remoteappmanager.restresources.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-remoteappmanager.restresources package
-======================================
-
-Submodules
-----------
-
-remoteappmanager.restresources.application module
--------------------------------------------------
-
-.. automodule:: remoteappmanager.restresources.application
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.restresources.container module
------------------------------------------------
-
-.. automodule:: remoteappmanager.restresources.container
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.restresources
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.rst b/doc/source/api/remoteappmanager.rst
deleted file mode 100644
index 4fc61bd24..000000000
--- a/doc/source/api/remoteappmanager.rst
+++ /dev/null
@@ -1,116 +0,0 @@
-remoteappmanager package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
-    remoteappmanager.cli
-    remoteappmanager.db
-    remoteappmanager.docker
-    remoteappmanager.handlers
-    remoteappmanager.logging
-    remoteappmanager.rest
-    remoteappmanager.restresources
-    remoteappmanager.services
-
-Submodules
-----------
-
-remoteappmanager.application module
------------------------------------
-
-.. automodule:: remoteappmanager.application
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.auth module
-----------------------------
-
-.. automodule:: remoteappmanager.auth
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.command_line_config module
--------------------------------------------
-
-.. automodule:: remoteappmanager.command_line_config
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.file_config module
------------------------------------
-
-.. automodule:: remoteappmanager.file_config
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.jinja2_adapters module
----------------------------------------
-
-.. automodule:: remoteappmanager.jinja2_adapters
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.netutils module
---------------------------------
-
-.. automodule:: remoteappmanager.netutils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.paths module
------------------------------
-
-.. automodule:: remoteappmanager.paths
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.spawners module
---------------------------------
-
-.. automodule:: remoteappmanager.spawners
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.traitlets module
----------------------------------
-
-.. automodule:: remoteappmanager.traitlets
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.user module
-----------------------------
-
-.. automodule:: remoteappmanager.user
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.utils module
------------------------------
-
-.. automodule:: remoteappmanager.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/remoteappmanager.services.rst b/doc/source/api/remoteappmanager.services.rst
deleted file mode 100644
index d3ef14ea8..000000000
--- a/doc/source/api/remoteappmanager.services.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-remoteappmanager.services package
-=================================
-
-Submodules
-----------
-
-remoteappmanager.services.hub module
-------------------------------------
-
-.. automodule:: remoteappmanager.services.hub
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-remoteappmanager.services.reverse_proxy module
-----------------------------------------------
-
-.. automodule:: remoteappmanager.services.reverse_proxy
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: remoteappmanager.services
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 61b673618..de5bb5da9 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -19,7 +19,11 @@
 #
 import os
 import sys
-sys.path.append(os.path.abspath('../../remoteappmanager'))
+sys.path.append(os.path.abspath('../../'))
+sys.path.append(os.path.abspath('.'))
+
+from mock_missing import mock_modules
+mock_modules()
 
 from remoteappmanager import __version__, MAJOR, MINOR
 from remoteappmanager.command_line_config import CommandLineConfig
@@ -41,6 +45,10 @@
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
     'traitlet_documenter',
+    # patched autosummary for issue
+    # https://github.com/sphinx-doc/sphinx/issues/1061
+    '_extensions'
+    #'sphinx.ext.autosummary'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -442,7 +450,24 @@
 
 with open(HELP_FILE_PATH, 'w') as fh:
     for name, traitlet in sorted(_config.traits().items()):
-        print('--{name:<30} {help}'.format(name=name, help=traitlet.help),
-              file=fh)
-
+        print(
+            '--{name:<30} {help}'.format(
+                name=name, help=traitlet.help), file=fh)
 del _config
+
+
+autodoc_member_order = 'source'
+autoclass_content = 'both'
+autodoc_default_flags = [
+    'show-inheritance', 'members', 'undoc-members']
+autosummary_generate = True
+
+# Patch sphinx to 1.4.x to suppress warning about nonlocal image URI
+import sphinx.environment
+from docutils.utils import get_source_line
+
+def _warn_node(self, msg, node, **kwargs):
+    if not msg.startswith('nonlocal image URI found:'):
+        self._warnfunc(msg, '%s:%s' % get_source_line(node), **kwargs)
+
+sphinx.environment.BuildEnvironment.warn_node = _warn_node
diff --git a/doc/source/developer.rst b/doc/source/developer.rst
index 9fadf573d..3b74ddd68 100644
--- a/doc/source/developer.rst
+++ b/doc/source/developer.rst
@@ -1,7 +1,57 @@
-Developer documentation
-=======================
+API reference
+=============
 
-.. toctree::
-   :maxdepth: 1
 
-   api
+RemoteAppManager
+----------------
+
+The main tornado web application that manages the containers (docker applications)
+for each user.
+
+.. autosummary::
+   :toctree: api
+   :template: module_template.rst
+
+   remoteappmanager.application
+   remoteappmanager.auth
+   remoteappmanager.command_line_config
+   remoteappmanager.file_config
+   remoteappmanager.jinja2_adapters
+   remoteappmanager.netutils
+   remoteappmanager.spawners
+   remoteappmanager.traitlets
+   remoteappmanager.user
+   remoteappmanager.utils
+   remoteappmanager.cli.remoteappdb.__main__
+   remoteappmanager.cli.remoteapprest.__main__
+   remoteappmanager.db.csv_db
+   remoteappmanager.db.interfaces
+   remoteappmanager.db.orm
+   remoteappmanager.docker.async_docker_client
+   remoteappmanager.docker.container
+   remoteappmanager.docker.container_manager
+   remoteappmanager.docker.image
+   remoteappmanager.handlers.base_handler
+   remoteappmanager.handlers.home_handler
+   remoteappmanager.logging.logging_mixin
+   remoteappmanager.restresources.application
+   remoteappmanager.restresources.container
+   remoteappmanager.services.hub
+   remoteappmanager.services.reverse_proxy
+
+
+REST tornado
+------------
+
+A generic implementation of Rest APIs using tornado.
+
+.. autosummary::
+   :toctree: api
+   :template: module_template.rst
+
+   remoteappmanager.rest.exceptions
+   remoteappmanager.rest.registry
+   remoteappmanager.rest.resource
+   remoteappmanager.rest.rest_handler
+   remoteappmanager.rest.http.payloaded_http_error
+
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 03a9a063a..38e424f1d 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -1,17 +1,8 @@
-Simphony-remote documentation
-=============================
+.. include:: ../../README.rst
 
-The Simphony-remote is web service that allows users to start and work with
-simphony enabled environments remotely.
 
-Key provided features:
-
-   - Isolated working environments using docker containers.
-   - No install remote access through a web browser.
-   - Sharing of working sessions.
-   - Based on community supported open source initiatives (JupyterHub)
-
-.. note:: More to come...
+Contents
+--------
 
 .. toctree::
    :maxdepth: 1
@@ -22,4 +13,8 @@ Key provided features:
    design
    developer
    troubleshooting
-   license
+
+License
+-------
+
+.. include:: ../../LICENSE.rst
diff --git a/doc/source/license.rst b/doc/source/license.rst
deleted file mode 100644
index 226f0dc36..000000000
--- a/doc/source/license.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-License
-=======
-
-.. include:: ../../COPYING.rst
diff --git a/doc/source/mock_missing.py b/doc/source/mock_missing.py
new file mode 100644
index 000000000..55fade065
--- /dev/null
+++ b/doc/source/mock_missing.py
@@ -0,0 +1,86 @@
+#------------------------------------------------------------------------------
+#
+#  Copyright (c) 2015, Enthought, Inc.
+#  All rights reserved.
+#
+#  This software is provided without warranty under the terms of the BSD
+#  license included in LICENSE.txt and may be redistributed only
+#  under the conditions described in the aforementioned license.  The license
+#  is also available online at http://www.enthought.com/licenses/BSD.txt
+#
+#  Thanks for using Enthought open source!
+#
+#------------------------------------------------------------------------------
+import sys
+
+
+def mock_modules():
+    """ Mock missing modules if necessary """
+
+    MOCK_MODULES = []
+    MOCK_TYPES = []
+
+    try:
+        import pwd
+    except ImportError:
+        MOCK_MODULES = ['pwd']
+        MOCK_TYPES = []
+    else:
+        del pwd
+
+    try:
+        import grp
+    except ImportError:
+        MOCK_MODULES.append('grp')
+    else:
+        del grp
+
+    try:
+        import pamela
+    except ImportError:
+        MOCK_MODULES.append('pamela')
+    else:
+        del pamela
+
+    TYPES = {
+        mock_type: type(mock_type, bases, {'__module__': path})
+        for path, mock_type, bases in MOCK_TYPES}
+
+    class DocMock(object):
+
+        def __init__(self, *args, **kwds):
+            if '__doc_mocked_name__' in kwds:
+                self.__docmock_name__ = kwds['__docmocked_name__']
+            else:
+                self.__docmock_name__ = 'Unknown'
+
+        def __getattr__(self, name):
+            if name in ('__file__', '__path__'):
+                return '/dev/null'
+            elif name == '__all__':
+                return []
+            else:
+                return TYPES.get(name, DocMock(__docmock_name__=name))
+
+        def __call__(self, *args, **kwards):
+            return DocMock()
+
+        def __iter__(self):
+            return self
+
+        def __next__(self):
+            raise StopIteration()
+
+        def next(self):
+            raise StopIteration()
+
+        @property
+        def __name__(self):
+            return self.__docmock_name__
+
+        def __repr__(self):
+            return '<DocMock.{}>'.format(self.__name__)
+
+    sys.modules.update(
+        (mod_name, DocMock(mocked_name=mod_name)) for mod_name in MOCK_MODULES)
+    print('mocking modules {} and types {}'.format(MOCK_MODULES, MOCK_TYPES))
diff --git a/doc/source/troubleshooting.rst b/doc/source/troubleshooting.rst
index 24fc89785..af883f0a3 100644
--- a/doc/source/troubleshooting.rst
+++ b/doc/source/troubleshooting.rst
@@ -1,6 +1,9 @@
 Troubleshoot
 ------------
 
+.. toctree::
+   :includehidden:
+
 .. include::
     troubleshoot/database.rst
 
diff --git a/tox.ini b/tox.ini
index 9881b3e05..575dd648d 100644
--- a/tox.ini
+++ b/tox.ini
@@ -11,4 +11,4 @@ commands=python -m tornado.testing discover -s tests -t . -v
 passenv = *
 
 [flake8]
-exclude = build/*,venv/*,doc/source/conf.py,tests/utils.py,selenium_tests/*
+exclude = build/*,venv/*,doc/source/*,tests/utils.py,selenium_tests/*